6ZIB

CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-1 (RPMFE1) COMPLEXED WITH ACETOACETYL-COA AND NADH


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5OMO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6295MES, pH 6; 16%w/v PEG 4000; 150mM ammonium sulfate. Co-crystallized with 2mM CoA
Crystal Properties
Matthews coefficientSolvent content
2.9357.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.937α = 90
b = 127.39β = 90
c = 228.173γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-08-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.972957ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.748.8895.50.1570.060.99511.77.775119952.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.781.0920.4060.6912

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5OMO2.748.8850871254094.5540.2340.23160.273372.958
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
6.068-1.042-5.026
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.071
r_dihedral_angle_4_deg20.304
r_dihedral_angle_3_deg17.798
r_lrange_it7.179
r_dihedral_angle_1_deg6.068
r_scangle_it1.156
r_mcangle_it1.086
r_angle_refined_deg1.081
r_scbond_it0.666
r_mcbond_it0.582
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.071
r_dihedral_angle_4_deg20.304
r_dihedral_angle_3_deg17.798
r_lrange_it7.179
r_dihedral_angle_1_deg6.068
r_scangle_it1.156
r_mcangle_it1.086
r_angle_refined_deg1.081
r_scbond_it0.666
r_mcbond_it0.582
r_nbtor_refined0.307
r_symmetry_nbd_refined0.246
r_nbd_refined0.208
r_symmetry_xyhbond_nbd_refined0.187
r_xyhbond_nbd_refined0.13
r_ncsr_local_group_10.097
r_chiral_restr0.095
r_bond_refined_d0.004
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11074
Nucleic Acid Atoms
Solvent Atoms67
Heterogen Atoms206

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing